Neha Patil


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Symbol  SecA
Pfam  structures
PDBsum  structure summary
Pfam  PF07517

The SecA protein is a cell membrane associated subunit of the eubacterial Sec or Type II secretory pathway, a system which is responsible for the secretion of proteins through the cell membrane. Within this system SecA has the functional properties of an ATPase and is required to empower the movement of the protein substrate across the translocon channel.


The translocase system encompasses an array of proteins which are functionally centred on the translocon channel which mediates the export of proteins across the bacterial cytoplasmic membrane and the insertion of membrane proteins into it. Regardless of the chosen targeting route, preprotein eventually reach the cytoplasmic membrane and make contact with the translocase. This translocase consists out of the peripheral membrane ATPase SecA and the translocon membrane channel composed out of the proteins SecY, SecE, and SecG. Conformational changes within the SecA structure are the effect of its ATP-hydrolyzing behaviour and possibly lead to the stepwise export of the preprotein substrate through the SecYEG channel.


SecA is a complex protein which structure consists out of six characterized domains that can explain SecA’s capabilities to bind substrates and to move them. The following five domains seem to be present in all SecA proteins that have been structurally analyzed so far.

DEAD motor domain

This amino acid domain is subdivided into the two nucleotide binding folds 1 and 2 (NBF1 and NBF2) where ATP is bound and hydrolyzed. The chemical energy from the phosphodiester bonds results in a conformational change which is transferred to other domains (especially the HWD and the PPXD domains) which consequently mechanically move the preprotein across the membrane. However, these conformational changes are partly regulated by other protomer domains described below.

C-terminal linker domain

The capability to bind to the SecB chaperone during post-translational translocation and to bind the phospholipid bilayer is important for SecA functioning and is achieved by the C-terminal linker domain.

Helical wing domain (HWD)

Located at the C-terminal portion of the molecule, this domain is in contact with the HSD and PPXD domains. Likely it plays a role in transferring molecular conformational motion, which it receives from HSD and which originates from ATP hydrolysis in the DEAD motor domain, to the PPXD domain.

Peptide cross linking domain (PPXD)

Since SecA’s essential function is the transport of preprotein across the membrane the ability to actually bind preprotein must be given. The PPXD domain fulfils this function upon substrate binding.

Helical scaffold domain (HSD)

This domain lies in the center of the SecA protomer and contacts via α-helical interactions all other subdomains. In addition it contains the intramolecular regulator of ATP hydrolysis 1 (IRA1) subdomain which seems to prevent unwanted ATP hydrolysis when SecA is not bound to SecYEG. Together with IRA1, a conserved salt bridge called Gate 1 might function to prevent unnecessary conformational change. Gate 1 seems to functionally connect the nucleotide (ATP) binding site of the DEAD motor domain with the PPXD domain which results in regulation of ATP hydrolysis only upon preprotein binding. However, this coordinative behaviour has only been shown to occur when SecA is bound to SecYEG.


SecA Wikipedia

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